Research workbench
Enterobacter cloacae GC1 class C beta-lactamase complexed with transition-state analog of cefotaxime
Analyse Enterobacter cloacae GC1 class C beta-lactamase complexed with transition-state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RGZ
- Type
- protein
- Length
- 363 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class C beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P05364
- Ligands
- PTX
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class C beta-lactamase (EC 3.5.2.6) | protein | 363 | 41% helix, 23% strand | P05364 |
Ligands and binding sites
- PTX · {[(2E)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)ethanoyl]amino}methylphosphonic acid · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.74 | 0.81 | 71 | PTX, GOL |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1RGZ · Enterobacter cloacae GC1 Class C beta-Lactamase Complexed with Transition-State Analog of… · the same entry in another collection · chain A against A, TM-score 1.00
- P05364 · AlphaFold monomer V2.0 prediction for beta-lactamase (P05364) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P05364
- Elsewhere: RCSB PDB 1RGZ · PDBe 1RGZ · UniProt P05364
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